Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
| Page standards status: Informative |
@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
<http://hl7.org/fhir/Observation/variant-with-molec-consequences> a fhir:Observation ;
fhir:nodeRole fhir:treeRoot ;
fhir:Resource.id [ fhir:value "variant-with-molec-consequences"] ;
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ;
fhir:index 0 ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>
]
] ;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ] ;
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation variant-with-molec-consequences</b></p><a name=\"variant-with-molec-consequences\"> </a><a name=\"hcvariant-with-molec-consequences\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-HG00403.html\">Alanine B. Everyone Unknown, DoB: 1951-01-20 ( Medical Record Number: m234 (use: usual, ))</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000001.10}\">NC_000001.10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6706-1}\">Heterozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81252-9}\">Discrete genetic variant</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NC_000001.10:g.86852621A>G}\">NC_000001.10:g.86852621A>G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample VAF</span></p><p><b>value</b>: 0.6 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic Ref allele [ID]</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Genomic Alt allele [ID]</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 92822-6}\">Genomic coord system</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30100-4}\">0-based interval counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Variant exact start-end</span></p><p><b>value</b>: 86852620-?</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 92821-8}\">Population allele frequency</span></p><p><b>value</b>: 0.327084 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</span></p></blockquote></div>"
] ;
fhir:Observation.status [ fhir:value "final"] ;
fhir:Observation.category [
fhir:index 0 ;
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ] ;
fhir:Coding.code [ fhir:value "laboratory" ]
]
], [
fhir:index 1 ;
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0074" ] ;
fhir:Coding.code [ fhir:value "GE" ]
]
] ;
fhir:Observation.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:69548-6 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "69548-6" ] ;
fhir:Coding.display [ fhir:value "Genetic variant assessment" ]
]
] ;
fhir:Observation.subject [
fhir:link <http://hl7.org/fhir/Patient/HG00403> ;
fhir:Reference.reference [ fhir:value "Patient/HG00403" ]
] ;
fhir:Observation.effectiveDateTime [ fhir:value "2023-06-01"^^xsd:date] ;
fhir:Observation.performer [
fhir:index 0 ;
fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
] ;
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:LA9633-4 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "LA9633-4" ] ;
fhir:Coding.display [ fhir:value "Present" ]
]
] ;
fhir:Observation.component [
fhir:index 0 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:48002-0 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "48002-0" ] ;
fhir:Coding.display [ fhir:value "Genomic source class" ]
]
] ;
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:LA6683-2 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "LA6683-2" ] ;
fhir:Coding.display [ fhir:value "Germline" ]
]
]
], [
fhir:index 1 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:48013-7 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "48013-7" ] ;
fhir:Coding.display [ fhir:value "Genomic reference sequence ID" ]
]
] ;
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ] ;
fhir:Coding.code [ fhir:value "NC_000001.10" ]
]
]
], [
fhir:index 2 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:53034-5 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "53034-5" ] ;
fhir:Coding.display [ fhir:value "Allelic state" ]
]
] ;
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:LA6706-1 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "LA6706-1" ] ;
fhir:Coding.display [ fhir:value "Heterozygous" ]
]
]
], [
fhir:index 3 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:81252-9 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "81252-9" ] ;
fhir:Coding.display [ fhir:value "Discrete genetic variant" ]
]
] ;
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ] ;
fhir:Coding.code [ fhir:value "NC_000001.10:g.86852621A>G" ] ;
fhir:Coding.display [ fhir:value "NC_000001.10:g.86852621A>G" ]
]
]
], [
fhir:index 4 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:81258-6 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "81258-6" ] ;
fhir:Coding.display [ fhir:value "Sample VAF" ]
]
] ;
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.6"^^xsd:decimal ] ;
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ] ;
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ] ;
fhir:Quantity.code [ fhir:value "1" ]
]
], [
fhir:index 5 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:69547-8 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "69547-8" ] ;
fhir:Coding.display [ fhir:value "Genomic Ref allele [ID]" ]
]
] ;
fhir:Observation.component.valueString [ fhir:value "A" ]
], [
fhir:index 6 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:69551-0 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "69551-0" ] ;
fhir:Coding.display [ fhir:value "Genomic Alt allele [ID]" ]
]
] ;
fhir:Observation.component.valueString [ fhir:value "G" ]
], [
fhir:index 7 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:92822-6 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "92822-6" ] ;
fhir:Coding.display [ fhir:value "Genomic coord system" ]
]
] ;
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:LA30100-4 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "LA30100-4" ] ;
fhir:Coding.display [ fhir:value "0-based interval counting" ]
]
]
], [
fhir:index 8 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:81254-5 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "81254-5" ]
] ;
fhir:CodeableConcept.text [ fhir:value "Variant exact start-end" ]
] ;
fhir:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "86852620"^^xsd:decimal ]
]
]
], [
fhir:index 9 ;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:92821-8 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "92821-8" ]
] ;
fhir:CodeableConcept.text [ fhir:value "Population allele frequency" ]
] ;
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.327084"^^xsd:decimal ] ;
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ] ;
fhir:Quantity.code [ fhir:value "1" ]
]
] .
<http://hl7.org/fhir/Patient/HG00403> a fhir:Patient .
<http://hl7.org/fhir/Organization/ExampleLab> a fhir:Organization .
# - ontology header ------------------------------------------------------------
<http://hl7.org/fhir/Observation/variant-with-molec-consequences.ttl> a owl:Ontology ;
owl:imports fhir:fhir.ttl ;
owl:versionIRI <http://build.fhir.org/Observation/variant-with-molec-consequences.ttl> .
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 4.0.1. Generated 2026-09-21
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